October 2021 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Test files for bug report [ChimeraX] #5467: AmiraMesh
by Tom Goddard 26 Oct '21

26 Oct '21

Hi Roden, These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only). Tom > On Oct 25, 2021, at 12:20 PM, Roden Deng Luo <deng.luo(a)kaust.edu.sa> wrote: > > Dear Tom and Andrea, > > Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name). > > Best regards, > Roden

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Open AmiraMesh 3.0 in ChimeraX
by Roden Deng Luo 25 Oct '21

25 Oct '21

Dear ChimeraX Users, I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date: 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the following error. First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'" Googling "AmiraMesh site:https://www.rbvi.ucsf.edu/pipermail/chimerax-users" shows no result. Can anyone kindly help here? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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problem with displaying secondary structures
by Elżbieta Wątor 24 Oct '21

24 Oct '21

Hi, I am trying to prepare figures for my publications and I have a problem with ss assignment. When I open structure in pymol, everything is assigned correctly. However, when I open the same structure in ChimeraX (1.2.5) I have gaps in helices and also not all of B strands are assigned correctly. I tried "dssp" command, but I probably type something wrong, because everytime I got "expected keyword" reply. Also I tried to do that manually using such commands setattr /B:5-7 res ss_type 1 and for some regions it works and for some not e.g I can change the whole helices with gaps to loop but in other way around it again gives me back helices with gaps. I've just started learning ChimeraX so probably there is some easy explanation, but I would be really grateful for your help. Best regards, Ela Wator

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red-cyan 3D view in chimera X?
by Maya Shmulevitz 22 Oct '21

22 Oct '21

Hi everyone, Does anyone know how to switch to red-cyan for the structures so that my class can see them with 3D red/cyan glasses? I used to do it on the old chimera with the camera feature but cannot find the option in chimera X. Thank you!! -- Maya Shmulevitz Canada Research Chair in Molecular Virology and Oncotherapy Associate Professor University of Alberta Medical Microbiology and Immunology Li Ka Shing Institute for Virology 6-21 HMRC Edmonton, Alberta, T6G 2E1 CANADA

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Running ChimeraX and a REPL
by Tom Mulvaney 21 Oct '21

21 Oct '21

Hi all, I'm wondering if anyone has any experience running ChimeraX with either a standard REPL or IPython REPL? ChimeraX already has a 'shell' tool that allows interacting with ChimeraX through a Python REPL which I've found invaluable for testing out ideas and poking around in ChimeraX in general. It would be really nice though if I could send Python code directly from my IDE to be evaluated. In order to make this work, it would be great if ChimeraX could be run from a terminal and provide a Python (or preferably IPython) REPL. As it stands, I've managed to nearly make this work with the following script: import IPython.terminal.embed IPython.terminal.embed.embed() I then run: ChimeraX --script repl.py After typing, `%gui qt5`, the ChimeraX GUI appears. I can then interact with the REPL directly from the comfort of Emacs and evaluate things - but! - the main 3D view does not end up being displayed. Does anyone know how to get the REPL and 3D stuff to work side-by-side? Kind regards, Tom

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ChimeraX issue
by Amaya Cuesta, Joan 20 Oct '21

20 Oct '21

Dear ChimeraX Team, I'm trying to use ChimeraX on my VM (Ubuntu 20.04.01), but I'm having the error on the screenshot attached below. I tried to update OpenGL to 3.3, and on the terminal it seems that it installed everything but then when I try to open again I'm getting the same issue. I tried to update OpenGL following this: https://www.reddit.com/r/Ubuntu/comments/8tpq05/how_can_update_my_display_d… But always when I do the command: glxinfo | grep "OpenGL version" , it shows: "OpenGL version string: 3.1 Mesa 21.0.3". Not sure why it is not updating to 3.3 while all the other packages are upgraded. Could you please advice? Kind regards Joan Cuesta (BSc) Viral Zoonoses Research Scientist Rabies and Viral Zoonoses Group Animal & Plant Health Agency (APHA) Internal extension: 71528 External: 02087201528 | Email: Joan.Cuesta(a)apha.gov.uk<mailto:Joan.Cuesta@apha.gov.uk> Website: www.gov.uk/apha<http://www.gov.uk/apha> | Twitter: @APHAgovuk<http://www.twitter.com/aphagovuk> | Facebook: aphagov<http://www.facebook.com/aphagov> Address: APHA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK Working hours - Monday - Friday, 9 - 5:30 pm Department for Environment, Food and Rural Affairs (Defra) This email and any attachments is intended for the named recipient only. If you have received it in error you have no authority to use, disclose, store or copy any of its contents and you should destroy it and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within Defra systems we can accept no responsibility once it has left our systems. Communications on Defra's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes.

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I Have a Problem Installing ChimeraX on Debian Buster
by Stephen P. Molnar 20 Oct '21

20 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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Remote Desktop usage
by Dmitry Semchonok 20 Oct '21

20 Oct '21

Dear colleagues, What could be the solution for the remote desktop of Chimera X user? One of the solution can be VNC but is there any other? Thank you Sincerely, Dmitry

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coil thickness
by Lisandro Otero 18 Oct '21

18 Oct '21

Dear Chimera developer; How can I change the coil thickness in a specific loop in ChimeraX? I have tried with the Hierarchical Specifiers but I was unsuccessful? Could you please give me a command line as example? I'm using “cartoon style coil thickness XX” Thanks in advance. Best. Dr. Lisandro H. Otero PhD. Leloir Institute Foundation Av. Patricias Argentinas 435 C1405BWE Buenos Aires, Argentina Phone: +054-11-5238-7500 ext. 2552 Fax: +054-11-5238-7501

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Feature suggestion - Models panel
by William Hofsøy 18 Oct '21

18 Oct '21

Hi, I would like to suggest/request that the "Models" panel should be able to rename models and change their ids from the list of models directly either through double click, like changing file names on windows, or through the right click context menu. Best regards, William

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ChimeraX-users October 2021